Where does OS X store the list of disabled fonts?

Where the list of disabled fonts is stored depends on the version of OS X you are using.

First of all, the ~/Library/Fonts Disabled/ and /Library/Fonts Disabled have never been used by Apple for the handling of disabled fonts; rather, fonts are simply deactivated in place: there's no need to move them out of the /Fonts/ folder in order to deactivate them. Those folders are most likely created by the Microsoft Office installer for Mac, or some other application installer.

As I mentioned, where the list of deactivated fonts is stored depends on the version of OS X you're using.

OS X 10.3: ~/Library/Preferences/com.apple.ATS.plist stores a list of file paths to the fonts which have been disabled in Font Book.

OS X 10.4 — 10.6: The enabled or disabled state of a particular font is stored within the font cache files themselves. There is no saved external record (like the preference file used in 10.3) of which fonts were disabled.

In OS X 10.7.x and later, while the enabled or disabled state of a particular font is still stored within the font cache files themselves, an external record of which fonts were disabled is stored in ~/Library/Preferences/com.apple.FontRegistry.user.plist.

I don't have Fonts Disabled folders either, but the list of disabled fonts is stored in ~/Library/Preferences/com.apple.FontRegistry.user.plist. If you copy it to another computer, run sudo atsutil databases -remove; atsutil server -shutdown to apply the changes.